Various functional groups of microorganisms and related biogeochemical processes are likely to control arsenic (As) mobilization in groundwater systems. However, spatially-dependent correlations between microbial community composition and geochemical zonation along groundwater flow paths are not fully understood, especially with respect to arsenic mobility. The western Hetao Basin was selected as the study area to address this limitation, where groundwater flows from a proximal fan (geochemical-group I: low As, oxidizing), through a transition area (geochemical-group II: moderate As, moderately-reducing) and then to a flat plain (geochemical-group III: high As, reducing). High-throughput Illumina 16S rRNA gene sequencing showed that the microbial community structure in the proximal fan included bacteria affiliated with organic carbon degradation and nitrate-reduction or even nitrate-dependant Fe(II)-oxidation, mainly resulting in As immobilization. In contrast, for the flat plain, high As groundwater contained Fe(III)- and As(V)-reducing bacteria, consistent with current models on As mobilization driven via reductive dissolution of Fe(III)/As(V) mineral assemblages. However, Spearman correlations between hydrogeochemical data and microbial community compositions indicated that ammonium as a possible electron donor induced reduction of Fe oxide minerals, suggesting a wider range of metabolic pathways (including ammonium oxidation coupled with Fe(III) reduction) driving As mobilization in high As groundwater systems.